Starting phenix.real_space_refine on Sun Apr 27 06:02:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8omu_16977/04_2025/8omu_16977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8omu_16977/04_2025/8omu_16977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8omu_16977/04_2025/8omu_16977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8omu_16977/04_2025/8omu_16977.map" model { file = "/net/cci-nas-00/data/ceres_data/8omu_16977/04_2025/8omu_16977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8omu_16977/04_2025/8omu_16977.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 3064 2.51 5 N 804 2.21 5 O 834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4737 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3842 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 25, 'TRANS': 471} Chain breaks: 2 Chain: "B" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 895 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Time building chain proxies: 3.87, per 1000 atoms: 0.82 Number of scatterers: 4737 At special positions: 0 Unit cell: (117.312, 68.224, 81.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 834 8.00 N 804 7.00 C 3064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.02 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 605.4 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 4 sheets defined 64.7% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.856A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 24 removed outlier: 3.533A pdb=" N LEU A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 132 through 160 removed outlier: 3.955A pdb=" N PHE A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 181 Processing helix chain 'A' and resid 184 through 214 removed outlier: 4.144A pdb=" N MET A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 removed outlier: 3.592A pdb=" N ALA A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 265 removed outlier: 3.847A pdb=" N LEU A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Proline residue: A 257 - end of helix removed outlier: 3.624A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.576A pdb=" N GLY A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 326 through 332 Processing helix chain 'A' and resid 332 through 358 Processing helix chain 'A' and resid 366 through 392 removed outlier: 4.259A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 394 through 415 removed outlier: 3.543A pdb=" N LEU A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 447 Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 484 through 501 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.574A pdb=" N ARG A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 56 removed outlier: 4.298A pdb=" N SER B 56 " --> pdb=" O SER B 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.238A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA3, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.575A pdb=" N LEU B 20 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR B 69 " --> pdb=" O GLN B 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.386A pdb=" N GLY B 10 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 109 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 92 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1491 1.34 - 1.46: 1127 1.46 - 1.58: 2178 1.58 - 1.70: 0 1.70 - 1.82: 55 Bond restraints: 4851 Sorted by residual: bond pdb=" CA GLN A 510 " pdb=" CB GLN A 510 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.44e+00 bond pdb=" C SER B 114 " pdb=" O SER B 114 " ideal model delta sigma weight residual 1.242 1.231 0.010 1.00e-02 1.00e+04 1.02e+00 bond pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.48e-01 bond pdb=" CA THR A 36 " pdb=" C THR A 36 " ideal model delta sigma weight residual 1.522 1.535 -0.013 1.37e-02 5.33e+03 8.51e-01 bond pdb=" C MET A 485 " pdb=" N PRO A 486 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.36e-02 5.41e+03 7.79e-01 ... (remaining 4846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 6489 2.11 - 4.23: 87 4.23 - 6.34: 12 6.34 - 8.45: 6 8.45 - 10.56: 2 Bond angle restraints: 6596 Sorted by residual: angle pdb=" O SER B 114 " pdb=" C SER B 114 " pdb=" N ALA B 115 " ideal model delta sigma weight residual 121.20 113.31 7.89 1.61e+00 3.86e-01 2.40e+01 angle pdb=" CA LYS A 297 " pdb=" CB LYS A 297 " pdb=" CG LYS A 297 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA GLN B 39 " pdb=" CB GLN B 39 " pdb=" CG GLN B 39 " ideal model delta sigma weight residual 114.10 121.02 -6.92 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CB MET A 464 " pdb=" CG MET A 464 " pdb=" SD MET A 464 " ideal model delta sigma weight residual 112.70 122.76 -10.06 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CA LEU A 18 " pdb=" CB LEU A 18 " pdb=" CG LEU A 18 " ideal model delta sigma weight residual 116.30 126.86 -10.56 3.50e+00 8.16e-02 9.11e+00 ... (remaining 6591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 2367 17.39 - 34.78: 352 34.78 - 52.17: 115 52.17 - 69.56: 14 69.56 - 86.95: 7 Dihedral angle restraints: 2855 sinusoidal: 1097 harmonic: 1758 Sorted by residual: dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual -86.00 -140.51 54.51 1 1.00e+01 1.00e-02 4.03e+01 dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual -86.00 -47.78 -38.22 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CA CYS A 49 " pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " ideal model delta sinusoidal sigma weight residual -73.00 -6.88 -66.12 1 2.00e+01 2.50e-03 1.43e+01 ... (remaining 2852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 435 0.026 - 0.053: 191 0.053 - 0.079: 75 0.079 - 0.106: 42 0.106 - 0.132: 12 Chirality restraints: 755 Sorted by residual: chirality pdb=" CA ASN A 125 " pdb=" N ASN A 125 " pdb=" C ASN A 125 " pdb=" CB ASN A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CG LEU A 434 " pdb=" CB LEU A 434 " pdb=" CD1 LEU A 434 " pdb=" CD2 LEU A 434 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 752 not shown) Planarity restraints: 824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " 0.043 2.00e-02 2.50e+03 8.02e-02 6.43e+01 pdb=" C SER B 114 " -0.139 2.00e-02 2.50e+03 pdb=" O SER B 114 " 0.050 2.00e-02 2.50e+03 pdb=" N ALA B 115 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 220 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C ALA A 220 " 0.036 2.00e-02 2.50e+03 pdb=" O ALA A 220 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 221 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 36 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C THR A 36 " 0.033 2.00e-02 2.50e+03 pdb=" O THR A 36 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 37 " -0.011 2.00e-02 2.50e+03 ... (remaining 821 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 886 2.76 - 3.30: 4667 3.30 - 3.83: 8318 3.83 - 4.37: 8848 4.37 - 4.90: 15563 Nonbonded interactions: 38282 Sorted by model distance: nonbonded pdb=" O MET A 23 " pdb=" OH TYR A 264 " model vdw 2.230 3.040 nonbonded pdb=" O PHE A 133 " pdb=" OH TYR A 185 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR A 451 " pdb=" OD1 ASP A 514 " model vdw 2.298 3.040 nonbonded pdb=" OE1 GLU B 35 " pdb=" OH TYR B 37 " model vdw 2.326 3.040 nonbonded pdb=" O LYS A 520 " pdb=" OG SER A 523 " model vdw 2.358 3.040 ... (remaining 38277 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.460 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4854 Z= 0.142 Angle : 0.650 10.565 6602 Z= 0.329 Chirality : 0.040 0.132 755 Planarity : 0.005 0.080 824 Dihedral : 18.005 86.945 1722 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.79 % Allowed : 35.56 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.36), residues: 604 helix: 1.35 (0.29), residues: 355 sheet: -1.36 (0.75), residues: 42 loop : -0.73 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.000 HIS A 130 PHE 0.012 0.001 PHE A 351 TYR 0.022 0.001 TYR A 354 ARG 0.008 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.14994 ( 289) hydrogen bonds : angle 5.65273 ( 849) SS BOND : bond 0.00445 ( 3) SS BOND : angle 0.55438 ( 6) covalent geometry : bond 0.00307 ( 4851) covalent geometry : angle 0.64981 ( 6596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.511 Fit side-chains REVERT: B 29 VAL cc_start: 0.5845 (OUTLIER) cc_final: 0.5645 (m) REVERT: B 90 ASP cc_start: 0.7781 (m-30) cc_final: 0.7430 (m-30) outliers start: 4 outliers final: 0 residues processed: 75 average time/residue: 0.1657 time to fit residues: 16.0787 Evaluate side-chains 74 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.0000 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.209532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.172816 restraints weight = 6150.297| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.25 r_work: 0.3908 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4854 Z= 0.133 Angle : 0.600 8.407 6602 Z= 0.308 Chirality : 0.040 0.137 755 Planarity : 0.004 0.030 824 Dihedral : 4.048 18.560 668 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.52 % Allowed : 31.04 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.36), residues: 604 helix: 1.36 (0.28), residues: 360 sheet: -1.21 (0.76), residues: 42 loop : -0.49 (0.47), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.001 HIS A 130 PHE 0.012 0.001 PHE A 351 TYR 0.021 0.001 TYR A 354 ARG 0.005 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 289) hydrogen bonds : angle 4.69215 ( 849) SS BOND : bond 0.00407 ( 3) SS BOND : angle 0.76129 ( 6) covalent geometry : bond 0.00291 ( 4851) covalent geometry : angle 0.59977 ( 6596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.486 Fit side-chains REVERT: B 90 ASP cc_start: 0.7696 (m-30) cc_final: 0.7056 (m-30) outliers start: 23 outliers final: 13 residues processed: 99 average time/residue: 0.1548 time to fit residues: 20.0302 Evaluate side-chains 87 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 102 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 9 optimal weight: 0.0000 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.209442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.173590 restraints weight = 6129.343| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.24 r_work: 0.3951 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4854 Z= 0.118 Angle : 0.570 8.626 6602 Z= 0.289 Chirality : 0.039 0.134 755 Planarity : 0.004 0.030 824 Dihedral : 3.871 17.607 667 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.30 % Allowed : 30.45 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.36), residues: 604 helix: 1.41 (0.29), residues: 361 sheet: -1.06 (0.78), residues: 42 loop : -0.40 (0.47), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.000 HIS A 130 PHE 0.011 0.001 PHE A 351 TYR 0.018 0.001 TYR A 354 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 289) hydrogen bonds : angle 4.52676 ( 849) SS BOND : bond 0.00276 ( 3) SS BOND : angle 0.59376 ( 6) covalent geometry : bond 0.00255 ( 4851) covalent geometry : angle 0.56989 ( 6596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7978 (ttp80) REVERT: B 82 GLN cc_start: 0.6076 (pp30) cc_final: 0.5577 (tm-30) REVERT: B 90 ASP cc_start: 0.7652 (m-30) cc_final: 0.7342 (m-30) outliers start: 27 outliers final: 15 residues processed: 105 average time/residue: 0.1659 time to fit residues: 22.6702 Evaluate side-chains 91 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 102 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 0.0370 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.210660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174665 restraints weight = 6173.145| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.19 r_work: 0.3944 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4854 Z= 0.124 Angle : 0.584 9.230 6602 Z= 0.294 Chirality : 0.040 0.148 755 Planarity : 0.004 0.029 824 Dihedral : 3.855 17.619 667 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.30 % Allowed : 30.84 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.36), residues: 604 helix: 1.48 (0.29), residues: 361 sheet: -0.98 (0.79), residues: 42 loop : -0.35 (0.47), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.002 0.001 HIS A 48 PHE 0.013 0.001 PHE A 351 TYR 0.018 0.001 TYR A 354 ARG 0.006 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 289) hydrogen bonds : angle 4.47172 ( 849) SS BOND : bond 0.00341 ( 3) SS BOND : angle 0.54459 ( 6) covalent geometry : bond 0.00274 ( 4851) covalent geometry : angle 0.58431 ( 6596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8348 (ttp80) cc_final: 0.8113 (ttp80) REVERT: A 390 ASN cc_start: 0.8144 (m-40) cc_final: 0.7941 (m-40) REVERT: B 90 ASP cc_start: 0.7498 (m-30) cc_final: 0.7190 (m-30) outliers start: 27 outliers final: 19 residues processed: 106 average time/residue: 0.1522 time to fit residues: 21.0010 Evaluate side-chains 99 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 102 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.205927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.169511 restraints weight = 6207.745| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.25 r_work: 0.3856 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4854 Z= 0.183 Angle : 0.634 10.137 6602 Z= 0.321 Chirality : 0.042 0.133 755 Planarity : 0.004 0.030 824 Dihedral : 4.007 17.500 667 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 6.88 % Allowed : 28.68 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.36), residues: 604 helix: 1.35 (0.28), residues: 361 sheet: -0.43 (0.74), residues: 52 loop : -0.37 (0.50), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 247 HIS 0.003 0.001 HIS A 130 PHE 0.015 0.002 PHE A 351 TYR 0.022 0.002 TYR A 354 ARG 0.007 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 289) hydrogen bonds : angle 4.52285 ( 849) SS BOND : bond 0.00622 ( 3) SS BOND : angle 0.75128 ( 6) covalent geometry : bond 0.00433 ( 4851) covalent geometry : angle 0.63355 ( 6596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8051 (ttp80) REVERT: A 390 ASN cc_start: 0.8281 (m-40) cc_final: 0.8040 (m-40) REVERT: B 90 ASP cc_start: 0.7652 (m-30) cc_final: 0.7230 (m-30) outliers start: 35 outliers final: 29 residues processed: 114 average time/residue: 0.1596 time to fit residues: 23.4712 Evaluate side-chains 108 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 102 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 30.0000 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 53 optimal weight: 0.0270 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.197757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.159994 restraints weight = 6215.684| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.41 r_work: 0.3763 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4854 Z= 0.192 Angle : 0.671 10.052 6602 Z= 0.335 Chirality : 0.042 0.137 755 Planarity : 0.004 0.032 824 Dihedral : 4.148 18.424 667 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.88 % Allowed : 28.88 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.36), residues: 604 helix: 1.22 (0.28), residues: 361 sheet: -1.09 (0.78), residues: 42 loop : -0.43 (0.48), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 247 HIS 0.003 0.001 HIS A 130 PHE 0.015 0.002 PHE A 351 TYR 0.021 0.002 TYR A 354 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 289) hydrogen bonds : angle 4.53571 ( 849) SS BOND : bond 0.00599 ( 3) SS BOND : angle 1.80636 ( 6) covalent geometry : bond 0.00458 ( 4851) covalent geometry : angle 0.66898 ( 6596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8457 (mt) REVERT: A 80 ARG cc_start: 0.8573 (ttp80) cc_final: 0.8044 (ttp80) REVERT: A 390 ASN cc_start: 0.8354 (m-40) cc_final: 0.8041 (m-40) REVERT: B 90 ASP cc_start: 0.7851 (m-30) cc_final: 0.7190 (m-30) outliers start: 35 outliers final: 28 residues processed: 112 average time/residue: 0.1580 time to fit residues: 22.9758 Evaluate side-chains 107 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.0770 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.205486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.168851 restraints weight = 6160.909| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.22 r_work: 0.3877 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4854 Z= 0.152 Angle : 0.636 10.819 6602 Z= 0.317 Chirality : 0.041 0.127 755 Planarity : 0.004 0.030 824 Dihedral : 4.078 17.566 667 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.50 % Allowed : 30.84 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.36), residues: 604 helix: 1.31 (0.28), residues: 362 sheet: -1.08 (0.79), residues: 42 loop : -0.40 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 346 HIS 0.003 0.001 HIS A 130 PHE 0.013 0.001 PHE A 351 TYR 0.021 0.001 TYR A 354 ARG 0.008 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 289) hydrogen bonds : angle 4.45701 ( 849) SS BOND : bond 0.00432 ( 3) SS BOND : angle 1.74238 ( 6) covalent geometry : bond 0.00353 ( 4851) covalent geometry : angle 0.63416 ( 6596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.504 Fit side-chains REVERT: A 8 LYS cc_start: 0.8578 (mmtm) cc_final: 0.8373 (mmtt) REVERT: A 29 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8537 (mt) REVERT: A 80 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8267 (ttp80) REVERT: A 390 ASN cc_start: 0.8348 (m-40) cc_final: 0.8056 (m-40) REVERT: B 60 TYR cc_start: 0.8108 (m-80) cc_final: 0.7628 (m-80) REVERT: B 90 ASP cc_start: 0.7671 (m-30) cc_final: 0.7218 (m-30) outliers start: 28 outliers final: 23 residues processed: 104 average time/residue: 0.1656 time to fit residues: 22.2191 Evaluate side-chains 102 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 5 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.208452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.171341 restraints weight = 6176.646| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.31 r_work: 0.3899 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4854 Z= 0.124 Angle : 0.619 11.197 6602 Z= 0.306 Chirality : 0.040 0.124 755 Planarity : 0.004 0.030 824 Dihedral : 3.982 17.513 667 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.50 % Allowed : 30.84 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.36), residues: 604 helix: 1.42 (0.28), residues: 363 sheet: -1.01 (0.78), residues: 42 loop : -0.36 (0.48), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 346 HIS 0.002 0.001 HIS A 130 PHE 0.011 0.001 PHE A 351 TYR 0.019 0.001 TYR A 354 ARG 0.008 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 289) hydrogen bonds : angle 4.37463 ( 849) SS BOND : bond 0.00328 ( 3) SS BOND : angle 1.51040 ( 6) covalent geometry : bond 0.00272 ( 4851) covalent geometry : angle 0.61796 ( 6596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.469 Fit side-chains REVERT: A 29 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8425 (mt) REVERT: A 80 ARG cc_start: 0.8312 (ttp80) cc_final: 0.8013 (ttp80) REVERT: A 390 ASN cc_start: 0.8262 (m-40) cc_final: 0.8005 (m-40) REVERT: B 60 TYR cc_start: 0.8053 (m-80) cc_final: 0.7605 (m-80) REVERT: B 90 ASP cc_start: 0.7443 (m-30) cc_final: 0.7062 (m-30) outliers start: 28 outliers final: 23 residues processed: 105 average time/residue: 0.1566 time to fit residues: 21.6742 Evaluate side-chains 101 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.205132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.168767 restraints weight = 6185.597| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.26 r_work: 0.3900 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4854 Z= 0.139 Angle : 0.637 11.435 6602 Z= 0.316 Chirality : 0.040 0.126 755 Planarity : 0.004 0.032 824 Dihedral : 3.984 17.506 667 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.50 % Allowed : 31.04 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.36), residues: 604 helix: 1.42 (0.28), residues: 361 sheet: -1.20 (0.75), residues: 42 loop : -0.29 (0.49), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 33 HIS 0.002 0.001 HIS A 130 PHE 0.013 0.001 PHE A 351 TYR 0.020 0.001 TYR A 354 ARG 0.008 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 289) hydrogen bonds : angle 4.40892 ( 849) SS BOND : bond 0.00493 ( 3) SS BOND : angle 1.59450 ( 6) covalent geometry : bond 0.00316 ( 4851) covalent geometry : angle 0.63552 ( 6596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.512 Fit side-chains REVERT: A 80 ARG cc_start: 0.8543 (ttp80) cc_final: 0.8305 (ttp80) REVERT: A 390 ASN cc_start: 0.8315 (m-40) cc_final: 0.8042 (m-40) REVERT: B 60 TYR cc_start: 0.8037 (m-80) cc_final: 0.7658 (m-80) REVERT: B 90 ASP cc_start: 0.7623 (m-30) cc_final: 0.7179 (m-30) outliers start: 28 outliers final: 23 residues processed: 102 average time/residue: 0.1611 time to fit residues: 21.6016 Evaluate side-chains 99 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 102 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 0.1980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.207336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.171379 restraints weight = 6114.971| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.25 r_work: 0.3940 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4854 Z= 0.124 Angle : 0.649 11.645 6602 Z= 0.319 Chirality : 0.040 0.141 755 Planarity : 0.004 0.033 824 Dihedral : 3.952 17.512 667 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.52 % Allowed : 31.83 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.36), residues: 604 helix: 1.40 (0.28), residues: 363 sheet: -1.22 (0.75), residues: 42 loop : -0.20 (0.49), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.001 0.000 HIS A 48 PHE 0.012 0.001 PHE A 351 TYR 0.019 0.001 TYR A 354 ARG 0.008 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 289) hydrogen bonds : angle 4.39934 ( 849) SS BOND : bond 0.00381 ( 3) SS BOND : angle 1.52044 ( 6) covalent geometry : bond 0.00271 ( 4851) covalent geometry : angle 0.64807 ( 6596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.545 Fit side-chains REVERT: A 80 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7981 (ttp80) REVERT: A 390 ASN cc_start: 0.8232 (m-40) cc_final: 0.7999 (m-40) REVERT: B 60 TYR cc_start: 0.7946 (m-80) cc_final: 0.7574 (m-80) REVERT: B 90 ASP cc_start: 0.7396 (m-30) cc_final: 0.7020 (m-30) outliers start: 23 outliers final: 22 residues processed: 95 average time/residue: 0.2025 time to fit residues: 25.2679 Evaluate side-chains 96 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.206490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.170421 restraints weight = 6226.583| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.27 r_work: 0.3928 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4854 Z= 0.132 Angle : 0.645 11.765 6602 Z= 0.318 Chirality : 0.040 0.125 755 Planarity : 0.004 0.033 824 Dihedral : 3.946 17.275 667 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.91 % Allowed : 31.63 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.36), residues: 604 helix: 1.38 (0.28), residues: 363 sheet: -1.28 (0.74), residues: 42 loop : -0.23 (0.49), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 33 HIS 0.002 0.001 HIS A 48 PHE 0.013 0.001 PHE A 351 TYR 0.019 0.001 TYR A 354 ARG 0.008 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 289) hydrogen bonds : angle 4.39422 ( 849) SS BOND : bond 0.00434 ( 3) SS BOND : angle 1.49874 ( 6) covalent geometry : bond 0.00295 ( 4851) covalent geometry : angle 0.64338 ( 6596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2727.88 seconds wall clock time: 48 minutes 32.63 seconds (2912.63 seconds total)